It should be possible to update the maintenance script so that it automatically deletes Flow pages that have an empty header and zero topics. I see you (Pppery) commented about that at phab:T371738#10286448 already, so I'm just confirming that it is being looked into by the team.
For the completely-empty pages, I wonder if we might want to delete them without-log-entry, so that the empty wikitext page doesn't have the "this page was deleted" banner at the top as a cluttering-distraction? I believe that is technically possible. --- If folks here agree that this is a good idea, then we can ask the team to make it so.
For the "almost empty" pages, I agree those would need to be examined manually. Personally, I agree with both of you that those pages can probably just be deleted, once they've been checked for edge-cases.
Thanks again for all your associated efforts and thoughts on this, Pppery! It's deeply appreciated.